spread_igraph_labels: Spread igraph node labels by angle from node center
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

spread_igraph_labels

R Documentation

Spread igraph node labels by angle from node center

Description

Spread igraph node labels by angle from node center

Usage

spread_igraph_labels(
  g,
  layout = NULL,
  y_bias = 1,
  update_g_coords = TRUE,
  do_reorder = TRUE,
  sortAttributes = NULL,
  nodeSortBy = c("x", "-y"),
  repulse = 3.5,
  force_relayout = FALSE,
  label_min_dist = 0.5,
  verbose = FALSE,
  ...
)

Arguments

`g`	igraph object
`layout`	numeric matrix representing the x and y coordinates of each node in `g`, in the same order as `V(g)`. When `layout` is not supplied, nodes are checked for attributes `c("x", "y")` which define a fixed internal layout. When `force_layout=TRUE` these coordinates are ignored. If that is not supplied, then `layout_with_qfr()` is called along with the `repulse` argument. Subsequent coordinates are stored in `V(g)$x` and `V(g)$y` when argument `update_g_coords=TRUE`.
`y_bias`	numeric value indicating the tendency to spread labels on the y-axis rather than symmetrically around each node. This argument elongates the circle surrounding a node into an ellipse with this ratio.
`update_g_coords`	logical indicating whether the layout coordinates will be stored in `graph_attr(g, "layout")`.
`do_reorder`	logical indicating whether to call `reorderIgraphNodes()` which re-distributes equivalent nodes based upon the node color(s). A node is "equivalent" to another node if both nodes have identical edges.
`sortAttributes`, `nodeSortBy`	arguments passed to `reorderIgraphNodes()` when `do_reorder=TRUE`.
`repulse`	argument passed to `layout_with_qfr()` only when `layout` is not supplied, and the layout is not stored in `c(V(g)$x, V(g)$y)`.
`force_relayout`	logical indicating whether the `igraph` layout should be recalculated, in order to override coordinates that may be previously stored in the `igraph` object itself. Note that when `layout` is supplied, it is always used.
`label_min_dist`	numeric value used to ensure all labels are at least some distance from the center. These units are defined by igraph, and are roughly in units of one line height of text.
`...`	additional arguments are passed to `layout_with_qfr()` when needed.

Details

This function uses the igraph vertex attribute "label.degree", which describes the angular offset for each vertex label. (The "label.degree" values are represented as radians, not degrees, starting at 0 for right, and proceeding clockwise starting from the right, down, left, top, right.)

This function requires a network layout, which must be fixed in order for the vertex labels to be properly oriented. Labels are oriented opposite the most dominant angular mean of edges from each network node. Typically the side of a node with the fewest edges has the most space to place a label. No further checks are performed for overlapping labels.

Note that this function only modifies the other important attribute "label.dist" when 'label_min_dist“ is defined, in order to enforce a minimum label distance from the center of each node. There is no other logic to position small or large labels to avoid overlapping labels.

Other jam igraph functions: cnet2df(), cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphBlanks(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()